One of the main reasons he was not informed was that he was in fact very opposed to the use of the bomb against Japan. The decision to use the bomb was actually very contentious and given MacArthur's particular concerns about reprisals during an occupation he was slated to oversee, he was purposely kept out of the loop.
"Shortly after "V-J Day," the end of the Pacific war, Brig. General Bonnie Fellers summed up in a memo for General MacArthur: "Neither the atomic bombing nor the entry of the Soviet Union into the war forced Japan's unconditional surrender. She was defeated before either these events took place."
Obviously no one wanted the attack to be made public and there was some danger that some of the people might in fact do so, so MacArthur was one who was kept out of the loop.
His feeling was that the bomb ought to be kept a secret as long as possible and used when absolutely necessary. Again, he felt Japan was no serious threat and would eventually surrender.